Sections wrapped in a shortcode do not appear in the TOC

support
3

Thank you! That set me off on the right track. I modified your partial and came up with this, which avoids using any JavaScript:

{{ $headers := findRE "<h[2].*?>(.|\n])+?</h[2]>" .Content   }}
{{ if and (ge (len $headers) 1) (ne $.Params.toc "none") }}
<div class="docs-right-nav">
    <div class="docs-right-nav-inner">
    <ul>
    {{ range $headers }}
    <!-- for each h2 element, do the following:
    - apply Hugo's plainify function to strip the html and get the contents
    - apply lower to turn it lowercase
    - replace whitespace with hyphens
    - strip punctuation -->
    <li><a href='#{{ replaceRE  "\\s" "-" (. | plainify | lower) | replaceRE "[,.!?;:]" "" }}'>{{ . | plainify }}</a></li>    
    {{ end }}
    </ul>
        <a class="js-download" href="index.pdf">Download page as PDF</a>
    </div>
</div>
{{ end }}

However, this is really just a workaround. I would love to know why Hugo does this - in my case, the shortcode did nothing to the headings, it was just around them.